Water quality standards (WQS) are derived to give scientifically-robust and legally-binding guidance on acceptable risks of chemical contaminants with a view to protecting aquatic ecosystems and biodiversity. In China, anthropogenic chemical pollution of water bodies is a major threat to aquatic life. China, therefore, urgently needs to establish a scientifically-robust, functional WQS system that will ensure chemical contaminants are maintained at acceptable levels that protect aquatic ecosystems. In this article, we review the significant need for comprehensive national-scale protection of aquatic ecosystems and the challenges associated with using the Environmental Quality Standards for Surface Water (GB3838−2002) to protect aquatic ecosystems in China. We have also summarized information about recent developments in the aquatic life criteria for freshwater ecosystems in China and in other jurisdictions. Finally, we have made recommendations for the future direction and development of WQS in China that could be tailored to suit regional environmental characteristics and native aquatic species so as to offer better, regional-specific protection to aquatic life in freshwater ecosystems.